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Table 2 An exploration of KEGG cancer pathways.

From: Concordant integrative gene set enrichment analysis of multiple large-scale two-sample expression data sets

  

Two data sets

Three data sets

KEGG cancer pathways

U/D

CES

Diff.

FDR

CES

Diff.

FDR

PPAR signaling *

down

0.671

>0.1

0.194

0.563

>0.1

0.210

MAPK signaling **

down

0.639

>0.1

0.209

0.857

>0.1

0.063

ERBB signaling *

up

0.629

>0.1

0.119

0.581

>0.1

0.188

Calcium signaling **

down

0.925

>0.1

0.051

0.694

>0.1

0.153

Cytokine-cytokine receptor interaction ***

down

0.717

>0.1

0.172

0.943

>0.1

0.022

Cell cycle ***

up

0.998

>0.1

<0.001

0.959

>0.1

0.012

p53 signaling ***

up

0.999

>0.1

<0.001

0.944

>0.1

0.018

MTOR signaling *

down

0.724

>0.1

0.167

0.611

>0.1

0.193

Apoptosis *

down

 

≤ 0.1

 

0.776

>0.1

0.102

WNT signaling ***

down

 

≤ 0.1

 

0.888

>0.1

0.048

TGF-β signaling

down

 

≤ 0.1

 

0.521

>0.1

0.236

VEGF signaling ***

down

0.784

>0.1

0.136

0.919

>0.1

0.033

Focal adhesion ***

up

>0.999

>0.1

<0.001

0.830

>0.1

0.077

ECM receptor interaction ***

up

0.996

>0.1

<0.001

0.977

>0.1

0.005

Adherens junction *

up

0.646

>0.1

0.114

 

≤ 0.1

 

JAK-STAT signaling ***

down

0.875

>0.1

0.082

0.901

>0.1

0.044

  1. Our application results for sixteen KEGG cancer pathways. "Diff" column presents the absolute difference between the CES based on up-regulated differential expression and the CES based on down-regulated differential expression. If "Diff"≤ 0.1, then no further analysis results is presented. Otherwise, the larger CES as well as the related FDR and differential expression direction (up or down) are presented in the "CES", "FDR" and "U/D" columns, respectively. Both application results (an integrative analysis of two data sets and an integrative analysis of three data sets) are presented for the listed pathways. Pathways with symbols *, ** or *** means that FDRs < 0.2, FDRs < 0.1 or FDRs < 0.05 are observed for at least one applications, respectively.